The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree

Lee, S. H. and Van der Werf, J. H. J. (2005) The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree. Genetics, 169 1: 455-466. doi:10.1534/genetics.104.033233


Author Lee, S. H.
Van der Werf, J. H. J.
Title The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree
Journal name Genetics   Check publisher's open access policy
ISSN 0016-6731
Publication date 2005-01
Sub-type Article (original research)
DOI 10.1534/genetics.104.033233
Volume 169
Issue 1
Start page 455
End page 466
Total pages 12
Place of publication Bethesda, MD, United States
Publisher Genetics Society of America
Language eng
Abstract Combined linkage disequilibrium and linkage (LDL) mapping can exploit historical as well as recent and observed recombinations in a recorded pedigree. We investigated the role of pedigree information in LDL mapping and the performance of LDL mapping in general complex pedigrees. We compared using complete and incomplete genotypic data, spanning 5 or 10 generations of known pedigree, and we used bi- or multiallelic markers that were positioned at 1- or 5-cM intervals. Analyses carried out with or without pedigree information were compared. Results were compared with linkage mapping in some of the data sets. Linkage mapping or LDL mapping with sparse marker spacing (∼5 cM) gave a poorer mapping resolution without considering pedigree information compared to that with considering pedigree information. The difference was bigger in a pedigree of more generations. However, LDL mapping with closely linked markers (∼1 cM) gave a much higher mapping resolution regardless of using pedigree information. This study shows that when marker spacing is dense and there is considerable linkage disequilibrium generated from historical recombinations between flanking markers and QTL, the loss of power due to ignoring pedigree information is negligible and mapping resolution is very high.
Keyword Pedigree information
Linkage mapping
Disequilibrium
Mapping
Genotypes
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Brain Institute Publications
 
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